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F L Suddath

Publications and source records attributed to F L Suddath.

30 records · Page 2Linked to original sources
PubMed1975

Yeast phenylalanine transfer RNA: atomic coordinates and torsion angles.

The atomic coordinates of yeast phenylalanine transfer RNA (tRNA) as well as the torsion angles of the polynucleotide chain are presented as derived from an x-ray diffraction analysis of orthorhombic crystals. A comparison is made between the coordinates obtained from analysis of monoclinic crystals of the same material. It is concluded that the molecule has substantially the same form in the orthorhombic and the monoclinic lattices, except for differences found between residues at the 3' end of the polynucleotides chain. A number of observations are made concerning hydrogen bonding interactions which may account for many of the residues conserved in all tRNA sequences.

Nucleic Acid Conformation↗
PubMed1974

Three-dimensional tertiary structure of yeast phenylalanine transfer RNA.

The 3-angstrom electron density map of crystalline yeast phenylalanine transfer RNA has provided us with a complete three-dimensional model which defines the positions of all of the nucleotide residues in the moleclule. The overall features of the molecule are virtually the same as those seen at a resolution of 4 angstroms except that many additional details of tertiary structure are now visualized. Ten types of hydrogen bonding are identified which define the specificity of tertiary interactions. The molecule is also stabilized by considerable stacking of the planar purines and pyrimidines. This tertiary structure explains, in a simple and direct fashion, chemical modification studies of transfer RNA. Since most of the tertiary interactions involve nucleotides which are common to all transfer RNA 's, it is likely that this three-dimensional structure provides a basic pattern of folding which may help to clarify the three-dimensional structure of all transfer RNA's.

Base Sequence↗
PubMed1974

The general structure of transfer RNA molecules.

The three-dimensional structure of yeast phenylalanine tRNA serves as a useful basis for understanding the tertiary structure of all tRNAs. A large number of tRNA sequences have been surveyed and some general conclusions are drawn. There are only a few regions in the molecule in which there are differences in the number of nucleotides; and the structure of yeast phenylalanine tRNA can accommodate these differences by forming or enlarging protuberances on the surface of the basic framework molecule. The nature and distribution of the differences in number of nucleotides are surveyed and possible hydrogen bonding interactions are discussed for a number of tRNA classes. The two most significant features of the molecule are the large number of stacking interactions which are seen to include most of the nucleotides in the molecule and the system of specific hydrogen bonding interactions. It is likely that these stabilizing elements are preserved in all tRNA structures.

Base Sequence↗
PubMed1974

The molecular structure of yeast phenylalanine transfer RNA in monoclinic crystals.

The molecular structure of monoclinic crystals of yeast phenylalanine tRNA is analyzed by comparing it to the orthorhombic crystals of the same material whose structure has been determined. Changing the packing of the molecule from the head-to-head, tail-to-tail arrangement in the orthorhombic lattice to a head-to-tail packing makes it possible to generate a proposed structure for the monoclinic unit cell. The structure factors for the proposed arrangement have been calculated and compared with those experimentally observed from monoclinic crystals. The residuals from this comparison are low enough to conclude that at 4-A resolution, the three-dimensional structure of the molecule in the monoclinic crystal is essentially the same as that in the orthorhombic crystal. In addition, a correlation coefficient calculated from intensities based on a skeletal model of the molecule also confirmed the structure in the monoclinic cell. Electron density difference maps, as well as the presence of close contacts in the anticodon loop region of the monoclinic crystal, suggest that the anticodon loop may have a slightly different conformation than that observed in the orthorhombic crystals.

Models, Structural↗
PubMed1973

Three-dimensional structure of yeast phenylalanine transfer RNA: folding of the polynucleotide chain.

At 4 A resolution the polynucleotides in yeast phenylalanine transfer RNA are seen in a series of electron dense masses about 5.8 A apart. These peaks are probably associated with the phosphate groups, while lower levels of electron density between segments of adjacent polynucleotide chains are interpreted as arising from hydrogen-bonded purine-pyrimidine base pairs. It is possible to trace the entire polynucleotide chain with only two minor regions of ambiguity. The polynucleotide chain has a secondary structure consistent with the cloverleaf conformation; however, its folding is different from that proposed in any model. The molecule is made of two double-stranded helical regions oriented at right angles to each other in the shape of an L. One end of the L has the CCA acceptor; the anticodon loop is at the other end, and the dihydrouridine and TpsiC loops form the corner.

Base Sequence↗
PubMed1972

The three-dimensional structure of yeast phenylalanine transfer RNA: shape of the molecule at 5.5-A resolution.

Three isomorphous heavy-atom derivatives have been obtained of orthorhombic crystals of phenylalanine transfer RNA from yeast. These derivatives contain osmium, samarium, and platinum. The positions of the heavy atoms have been determined; these have been used to calculate a three-dimensional electron-density map of transfer RNA at a resolution of 5.5 A. The map shows a high contrast between the molecular boundaries and the solvent areas, so that most of the external shape of the molecule can be determined. The molecule appears to be 92 A long and to have a width varying from 16 A to 34 A. There are some narrow regions in the molecule that connect more globular regions. The electron density map shows chains of dense objects approximately 6 A apart that are probably due to adjacent phosphate groups on the polynucleotide chain. At the present stage of the analysis it is not possible to trace the entire backbone unambiguously; however, the data at this resolution suggest no apparent similarity between the folding of the molecule and any of the tertiary structure models proposed for transfer RNA.

Models, Structural↗
PubMed1971

High-resolution x-ray diffraction patterns of crystalline transfer RNA that show helical regions.

Yeast phenylalanyl transfer RNA crystallizes in a simple orthorhombic unit cell (a = 33.2, b = 56.1, c = 161 A), and the crystal yields an x-ray diffraction pattern with a resolution of 2.3 A. From an analysis of the packing in the unit cell it is concluded that the molecular dimensions are approximately 80 by 33 by 28 A. The diffraction pattern viewed along the a-axis has a distribution characteristic of double-helical nucleic acids. However, this distribution is not found when the pattern is viewed along the b-axis. This has been interpreted as indicating that the double-helical portions of the transfer RNA molecule are approximately half a helical turn in length, and therefore can contain 4-7 base pairs. These results are consistent with the cloverleaf formulation of transfer RNA secondary structure.

Crystallization↗